Changes between Initial Version and Version 1 of COT12

Timestamp:

Apr 20, 2012, 12:22:25 PM (14 years ago)

Author:

tef

Comment:

--

COT12

@@ +1 @@
+---------------------------------------------------------------------------
+2011/2012 report
+---------------------------------------------------------------------------
+
+May 2, 2011
+  Lunch Talk to Faculty, SFLD and enzyme function annotation, Dept. of Bioengineering & Therapeutic Sciences, UCSF, 8 hours prep time, 8 attendees.
+  - Patsy Babbitt
+
+May 19, 2011
+  Cytoscape User Tutorial given at the Cytoscape Retreat in San Diego.  Had about 60 participants. Total
+  prep time was about 10 hours.
+  - Scooter Morris
+
+May 24, 2011
+  Interview and HIV capsid demonstration for an [http://connectedsocialmedia.com/6518/future-lab-3d-molecular-visualization/ NPR Future Lab podcast] sponsored by Intel Research on molecular visualization.  Showed NPR reporter Deirdre Kennedy 3d stereo visualization and answered questions.  Prep and delivery 5 hours.
+  - Tom Ferrin, Elaine Meng, Tom Goddard
+
+May 24, 2011
+  SFLD new feature presentation at EFI May Meeting in San Francisco. ~6 hours prep time and ~60 participants.
+  - Florian Lauck
+
+May 24, 2011
+  SFLD new progress and future plans at EFI May Meeting in San Francisco. ~6 hours prep time and 15 participants.
+  - Patsy Babbitt
+
+June 8, 2011
+  Cytoscape and Proteomics.  Training class given at UCSF to 8-10 UCSF campus researchers doing proteomics, specifically using MassSpec-based approaches.  Total prep time was 5 hours.
+  - Scooter Morris
+
+June 23, 2011
+  [http://www.cgl.ucsf.edu/chimera/hiv-core-june2011/hivcore.html HIV capsid demonstration] given to 10 high school students from [http://momagic.org Mo' MAGIC] program organized by UCSF Science and Health Education Partnership (SEP).  Showed 3-d stereo visualization, space navigator, plastic models in visualization vault.  Prep and delivery 5 hours.
+  - Tom Goddard
+
+June 26 - July 1, 2011
+  Chimera [http://www.cgl.ucsf.edu/chimera/3dem-june2011/fitdemo.html fitting talk] demonstrating global, sequential and symmetric fitting at [http://www.grc.org/programs.aspx?year=2011&program=threedim 3D EM Gordon conference], 200 participants, New Hampshire.  Also 2 hour Chimera question and answer session with 20 participants.  Prep and delivery 20 hours.
+  - Tom Goddard
+
+July 11-12, 2011
+  [http://edu.isb-sib.ch/course/view.php?id=97 Cytoscape User Tutorial and Developer's Workshop] at the Swiss Institute of Bioinformatics (SIB).  50 participants.  Total prep time was 20 hours.
+  - Scooter Morris
+
+July 15, 2011
+  Helped organize the [http://www.iscb.org/ismbeccb2011-program/satellite-meetings#network Network Biology SIG] at ISMB 2011 in Austria, Vienna.  Total participants: 160.
+  - Scooter Morris
+
+July 16, 2011
+  Gave a [http://www.iscb.org/ismbeccb2011-program/tutorials#pm5 Tutorial on Network Biology and Cytoscape] at ISMB 2011 in Austria, Vienna.  Total participants: 35.  Total prep time was 40 hours.
+  - Scooter Morris
+
+July 18, 2011
+   Gave an invited talk on user interface development in the [https://www.iscb.org/ismbeccb2011-program/workshops#w3 Data Visualization and User Interfaces] workshop at ISMB.  Total participants: 140.  Total prep time was 40 hours.
+  - Scooter Morris
+
+July 26, 2011
+  Society for Industrial Microbiology, New Orleans, SFLD intro and discussion, 8 hours prep time, 45 attendees.
+  - Patsy Babbitt
+
+July 28, 2011
+  Hosted the [http://cosmos.ucdavis.edu/ COSMOS kids] from UC Davis' Summer School for Math and Science. Viewed virus capsids in Chimera, influenza hemagglutinin conformational change. Total participants: 21.  Total prep/organizational time: 20 hours.
+  - Scooter Morris
+
+August 16, 2011
+  [http://www.ucsf.edu/news/2011/07/10230/ucsf-lead-first-annual-bay-area-science-festival Bay Area Science Festival]
+  publicity event demonstrations for House of Representatives Minority Leader
+  Nancy Pelosi and San Francisco Mayor Ed Lee.  Showed HIV capsid visualization.  Visualization Vault room.
+  10 guests and press.  4 hours preparation.
+  - Tom Goddard
+
+September 20, 2011
+  Two hiv capsid visualization demonstrations, 30 minutes each, for
+  [http://scienceonthemove.wordpress.com/2011/08/12/hello-world/ 22 Swiss high school students]
+  who won the Swiss
+  [http://www.simplyscience.ch/desktopdefault.aspx/tabid-335/admin-1/ "Science on the Move"]
+  national science competition sponsored by Roche and Genentech.  Arranged by Susan Jacobson at UCSF.
+  Prep time 4 hours.
+  - Tom Goddard
+
+September 21, 2011
+  Introduced SFLD in lecture for BMI206 core graduate course in bioinformatics, Biological and Medical Informatics Graduate Program, 15 hours prep time and 20 students.
+  - Patsy Babbitt
+
+September 23, 2011
+  Cytoscape Lab on the annotation of new enzyme functions using SFLD examples and data, BMI206 core graduate course in bioinformatics, Biological and Medical Informatics Graduate Program. 2 hours prep time and 20 students.
+  - Patsy Babbitt
+
+September 30, 2011
+  35-minute presentation to >25 students in UCSF BP204, "Macromolecular Interactions
+  and Assemblies" class.  Included 5 min on history of Computer Graphics Lab, the remainder
+  a Chimera demonstration: basic usage, morphing, viewing sequences, showing attribute
+  values, building multimers, stereo.  Prep time 16 hours including updating the previous
+  year's presentation, testing with the current version of Chimera, rehearsing the demo, 
+  preparing handouts, working through the homework assignment with current version of Chimera 
+  and making a "cheat sheet" for the TAs of commands that could be used for that homework.
+  - Elaine Meng, Eric Pettersen, Tom Goddard
+
+October 18, 2011
+  Talk to new iPQB (Integrative Program in Quantitative Biology) graduate students, UCSF, SFLD intro and discussion, 8 hours prep time, 45 attendees.
+  - Patsy Babbitt
+
+October 19, 2011
+  Talk to new PSPG (Pharmaceutical Sciences and Pharmacogenomics) graduate students, UCSF, SFLD intro and discussion, 4 hours prep time, 12 attendees.
+  - Patsy Babbitt
+
+October 22, 2011
+  Talk at joint UCB/UCSF graduate student retreat, Lake Tahoe, SFLD intro and discussion, 8 hours prep time, 100 attendees.
+  - Patsy Babbitt
+
+November 2, 2011
+  Bay Area Science Festival 20 minute demonstration of HIV capsid visualization for 10 Balboa High School
+  students. Presented in visualization vault room.
+  - Scooter Morris
+
+November 13, 2011
+  Lecture for BioE 280: joint UCB/UCSF graduate seminar series, SFLD intro and discussion, 5 hours prep time, 30
+attendees.
+  - Patsy Babbitt
+
+November 30, 2011
+  Hands-on Chimera tutorial at Purdue University.  90 minutes, 25 participants, 8 hours preparation.
+  Organized by Michael Rossmann.  Covered building a ParM filament using an EM map and Xray stucture.
+  - Tom Goddard
+
+November 30, 2011
+  Structural Biology Seminar talk at Purdue University, by invitation of Michael Rossmann.
+  1 hour, 45 in audience, 16 hours preparation.  Demonstrated hypothetical modeling of alpha
+  crystallin and HIV capsid and RNA.
+  - Tom Goddard
+
+November 30, 2011
+  SFLD new feature presentation at EFI November-December Meeting in San Francisco. ~3 hours prep time
+and ~40 participants.
+  - Florian Lauck
+
+November 30, 2011
+  SFLD new progress and future plans at EFI Advisory Committee Meeting in San Francisco. ~6 hours prep time and 25 participants.
+  - Patsy Babbitt
+
+December 1, 2011
+  Chimera hands-on training at Indiana University.  2.5 hours, 30 participants primarily undergraduates,
+  8 hours preparation.  Organized by David Morgan.  Covered alpha crystallin model building using Xray
+  structures and an EM map.  90 minute follow-along tutorial, 60 minute question and answer session on all
+  Chimera topics.
+  - Tom Goddard
+
+December 6, 2011
+  Chimera demonstration for University of San Francisco biochemistry class.  30 minutes, 8 participants,
+  4 hours preparation.  USF teacher Willie Melaugh.  Showed pombe cell x-ray tomography and dipeptide epimerase
+  enzyme structure which performs a step in recycling bacterial peptidoglycan cell wall.
+  - Tom Goddard, Elaine Meng
+
+January 9, 2012
+  Stereo visualization demonstration for Li Ka Shing Foundation, Solina Chau and 5 others. HIV core particle.
+  20 minute demo, 2 hours preparation and delivery.  Organized by Michael Faber.
+  - Tom Goddard, Tom Ferrin
+
+February 2, 2012
+  Talk on Network Biology at the Institute Pasteur.  Hosted by Benno Schwikowski.  Talk was 45 minutes with
+  15 minutes of Q&A.  Had 30-35 participants.  About 2 hours of preparation.
+  - Scooter Morris
+
+February 10, 2012
+  HIV visualization demonstration for UCSF iPQB candidate students.  5 students, 30 minutes demo, 2 hours
+  preparation and delivery.  Organized by Rebecca Brown.
+  - Tom Goddard
+
+February 17, 2012
+  HIV visualization demonstration for UCSF iPQB candidate students.  5 students, two 30 minute demonstrations,
+  2 hours preparation and delivery.  Organized by Rebecca Brown.
+  - Tom Goddard
+
+February 23, 2012
+  HIV visualization and stereo demonstrations for VIP guests attending the Byer's Lecture Celebration.
+  30 guests split in 3 groups, 10 minute demonstrations for each group, 3 hours preparation.  Organized
+  by Michael Faber of the UCSF donor development office.
+  - Tom Goddard, Tom Ferrin
+
+February 26-27, 2012
+  Planetarium dome animation at the 2012 Biophysical Society meeting in San Diego. Created 6 minute
+  [http://www.cgl.ucsf.edu/chimera/data/hiv-rna-jan2012/story.html animation] shown several times over two days in the
+  [http://www.biophysics.org/2012meeting/Program/SpecialFunctions/BiomolecularDiscoveryDome/tabid/3857/Default.aspx biomolecular discovery dome].  Molecular machines that replicate HIV RNA. 20 days production effort.
+  Organized by Wah Chiu, Matt Daugherty and Ed Egelman.
+  - Tom Goddard, Tom Ferrin
+
+March 5, 2012
+  Chimera tutorial at the VizBI conference in Heidelberg, Germany.  Tutorial covered basics of molecular visualization and molecular animation.  Total duration, 3 hours.  10 participants.  8 hours preparation time.
+  - Scooter Morris, Graham Johnson
+
+March 5, 2012
+  Cytoscape plugin development tutorial at the VizBI conference in Heidelberg, Germany.  Total duration, 3 hours.  20 participants.  8 hours preparation time.
+  - Scooter Morris
+
+March 12-13, 2012
+  Cytoscape tutorial at the Swiss Institute of Bioinformatics in Lausanne.  Total duration: 2 days.  40 participants.
+  - Scooter Morris
+